Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO356_24390 AO356_24390 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 AO356_24390
bifunctional aconitate hydratase 2/2-methylisocitrate
dehydratase
Length = 869
Score = 1377 bits (3563), Expect = 0.0
Identities = 667/859 (77%), Positives = 761/859 (88%), Gaps = 3/859 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
+LE YRKH+ ERAA GI P+PL+A Q A L+ELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL+A+AKG+A+SPLL ++A+ELLGTMQGGYNI L++ LDDA+LAP+AAK L
Sbjct: 61 AYVKAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLDDAELAPVAAKELK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKAK GN +AK V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAKAVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GI PD+ G GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGKTGPMKQIEEMRGQGFPIAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDD+P VPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPFVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
++MGDVID+YP+ G+V H T E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MHMGDVIDLYPHAGKVCKHGTDEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGLP D+F++ + AES +GF+LAQKMVG+ACG+ +G+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLPAFDLFKKPEAPAESTKGFTLAQKMVGKACGLAEGQGVRPGTYCEPKMTTVGSQDTT 420
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDG 480
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
+IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GKM+PGITLRDLVHAIP +AI+ GLLTVEKKGKKN FSGRILEIEGL L +EQAFEL+D
Sbjct: 541 GKMKPGITLRDLVHAIPYFAIQNGLLTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSD 600
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGCTIKL+KE I EYL SNI LL+WMI EGYGD RTLERR Q ME W+ANP+L
Sbjct: 601 ASAERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWVANPQL 660
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
+EADADAEYA VI+IDLADI EP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 MEADADAEYAEVIEIDLADISEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLL+ KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
RV +TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY Y ++D A
Sbjct: 781 RVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYAGKIDSMA 840
Query: 838 VDTYRYLNFNQLSQYTEKA 856
D YRYL+F+Q++++ E A
Sbjct: 841 ADVYRYLSFDQIAEFREAA 859
Lambda K H
0.317 0.136 0.400
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2150
Number of extensions: 76
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 865
Length of database: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space: 680621
Effective search space used: 680621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)
Align candidate AO356_24390 AO356_24390 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (EC 4.2.1.3))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR00117.hmm
# target sequence database: /tmp/gapView.2338.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00117 [M=844]
Accession: TIGR00117
Description: acnB: aconitate hydratase 2
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1527.1 0.0 0 1526.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 AO356_24390 bifunctional aconita
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 AO356_24390 bifunctional aconitate hydratase 2/2-methylisocitrate deh
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1526.9 0.0 0 0 1 844 [] 1 857 [. 1 857 [. 0.99
Alignments for each domain:
== domain 1 score: 1526.9 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayv 63
+le+yrkh+ eraa+gi p+plna+q+a l+ellkn+p++ee+fl++l+++rvppgvdeaayv
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEAAYV 63
69************************************************************* PP
TIGR00117 64 kagflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktll 126
kagfl+a+akg+++spl+ ++avellgtm+ggyn+ +l+e+l+ d+++a++aak l++tll
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 64 KAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLD--DAELAPVAAKELKHTLL 124
********************************************..***************** PP
TIGR00117 127 vfdafddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapd 188
+fdaf+dv+e++k n +ak vl+swa++ewf n++ la+ki+ vfkv+getntddlspapd
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 125 MFDAFHDVAEKAKNgNVHAKAVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTDDLSPAPD 187
************998************************************************ PP
TIGR00117 189 aftrpdiplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksat 241
a++rpdiplhalamlk ++++i + +i++++ +g+p+ayvgdvvgtgssrksat
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 188 AWSRPDIPLHALAMLKMARDGIVPdeqgktgpmkQIEEMRGQGFPIAYVGDVVGTGSSRKSAT 250
*********************999999************************************ PP
TIGR00117 242 nsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypyk 304
nsvlwf+g+d+pfvpnkragg+++g kiapif+nt+ed+galpie dv+++++gdvi++yp+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 251 NSVLWFFGDDVPFVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSNMHMGDVIDLYPHA 313
*************************************************************** PP
TIGR00117 305 geitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapa 366
g++ ++ t ev++tf++k+ +lldevraggripliigrglt+kar lgl+ ++fkk++apa
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 314 GKVCKHGTdEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPAFDLFKKPEAPA 376
******9999***************************************************** PP
TIGR00117 367 esakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdad 426
es+kgftlaqk+vgkacg+ +g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf+ad
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 377 ESTKGFTLAQKMVGKACGLaegQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSAD 439
******************86668**************************************** PP
TIGR00117 427 lvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdsh 489
lv+qsfchtaaypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdsh
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 440 LVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSH 502
*************************************************************** PP
TIGR00117 490 trfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkgl 552
trfp+gisfpagsglvafaaatgvmpldmpes+lvrfkg+++pgitlrdlv+aipy+ai++gl
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 503 TRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGKMKPGITLRDLVHAIPYFAIQNGL 565
*************************************************************** PP
TIGR00117 553 ltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksniv 615
ltvekkgk+n f+grileiegl l +eqafel+dasaersaagctikl+ke++ eyl+sni
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 566 LTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSDASAERSAAGCTIKLSKESITEYLQSNIT 628
*************************************************************** PP
TIGR00117 616 llkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndp 678
ll++mi egy+d+rtl+rr +ame+w+anp+l+eadadaeya+vieidla+i ep+l+apndp
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 629 LLRWMIGEGYGDARTLERRAQAMEAWVANPQLMEADADAEYAEVIEIDLADISEPVLCAPNDP 691
*************************************************************** PP
TIGR00117 679 ddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmdeqqliee 740
dd++lls vag++idevfigscmtnighfraagk+le+ k ++++rlw+ ppt+md++ql+ee
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 692 DDARLLSSVAGEKIDEVFIGSCMTNIGHFRAAGKLLEQVKgQLPTRLWLSPPTKMDAHQLTEE 754
*************************************9988********************** PP
TIGR00117 741 gyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaava 803
gyy+i+g+agar+e+pgcslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saela+va
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 755 GYYGIYGKAGARMEMPGCSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVA 817
*************************************************************** PP
TIGR00117 804 allgkiptkeeylalvsekvesakdklyrylnfnelenfee 844
++lg++pt+eey+++ + + a d +yryl f+++ +f+e
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_24390 818 SILGRLPTVEEYMEYAGKIDSMAAD-VYRYLSFDQIAEFRE 857
***************8877766666.************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (869 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.37
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory